rs768825050
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_003401.5(XRCC4):c.673C>T(p.Arg225Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,611,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. R225R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_003401.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRCC4 | NM_003401.5 | c.673C>T | p.Arg225Ter | stop_gained | 6/8 | ENST00000396027.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC4 | ENST00000396027.9 | c.673C>T | p.Arg225Ter | stop_gained | 6/8 | 5 | NM_003401.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151888Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250908Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135618
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1459776Hom.: 0 Cov.: 30 AF XY: 0.0000317 AC XY: 23AN XY: 726220
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151888Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74202
ClinVar
Submissions by phenotype
Short stature, microcephaly, and endocrine dysfunction Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 23, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at